They should be mixed. Since the chips are marked on the front side, you can mix them, distribute them face down, and separate them again after the game is finished. If the cards weren’t supposed to be mixed, different card backs would have been used to distinguish the cards.

As in all Catan games, you must meet the requirement only when you build. You don’t have to reverse previous building activities if later in the game you no longer have the things needed to meet the requirement.

No. No matter how many colony intersections remain free in the Catanian colonies after the starting setup, you are not allowed to found additional colonies in the Catanian colonies afterwards - not even if the requirement that in a 3-player game in each planetary system one colony intersection must remain free were met, and this requirement need not be met during the starting setup.